Sounds like corn subsidies were the driving force for Daschle's support rather than Thune. Daschle talks big but is willing to buck the Dem special interests for his own state - recall last summer when he tried (succeeded?) in getting forest cutting measures snuck through for SD but no one else, risking the enviros wrath.
As for Thune it still isn't clear that he is running. When Daschle announcing he was running instead of retiring it was noted that they were confident Thune wasn't going to run.

But would he buck his fellow SEnators if he weren't scared of a Senate challenger?

He's the big man (insert height joke here) of the Senate Dems so maybe. The Energy bill seems to be chock full of special interest items (i.e. ethanol) that would gain Dem senator support.

Forgot to note that nrsc.org has an story dated 11/19 noting that the GOP is still trying to get Thune to run.

Other than Daschle's sop, the energy bill is pure pork for Republicans. Complete waste of government resources, our money, and the paper it'll be printed on.

How many joules of fossil fuel does it take to grow and harvest a joule of corn ethanol?

Daschle probably didn't think he was "risking Cleeland's seat" on the civil service vote. He probably thought that Cleeland's Vietnam service would allow him to escape any criticism on questionable votes... much as I loathe Tommy Boy's politics, I have to concede he's usually much better tactically than that (e.g. the fire bill mentioned earlier, he voted for the partial birth ban while simultaneously blocking judges who wouldn't overturn it, etc.)

Gideon:

According to the US Dept of Agriculture, for every Btu used to produce ethanol, there are 1.34 Btu's made available.

Interestingly, the comparable figure for gasoline is .74, meaning that humans use more energy to produce gasoline, than can be harnessed by burning it.